Botany picture #66: Banksia heliantha

Banksia heliantha (Proteaceae), Australian National Botanic Garden, 2013. This species used to be known as Dryandra quercifolia but was transferred to Banksia in 2007. As in the case of the Epacridaceae being nested within the Ericaceae, it was discovered that Dryandra was nested within Banksia, and thus the former genus was sunk into the latter. And as in the case of the epacrids, in my eyes this should never really have been controversial. Epacrids look just like Ericaceae s.str. except they have lost one ring of stamens. Dryandras look just like Banksias s.str. except they have short head-like inflorescences instead of longer spike-like ones - the difference is merely how long a number of internodes in the inflorescence are.

A staff member of the ANBG once brought me a pot of a Dryandra as demonstration material for a talk and when he put it down, he said "I have never seen this species before, is it a Banksia?" No further comment needed.

Botany picture #65: Epacris impressa

Epacris impressa (Ericaceae), Australian National Botanic Garden, 2013. Here in Australia every state has an official state flower, and this is the one of Victoria. Not sure if German states have any; if so, it is at least not common knowledge. I guess if Germany as a whole has a national plant it is the oak. Here in Australia the national floral emblem is a wattle (Acacia, Fabaceae).

Where to submit a manuscript

In the past few weeks I have repeatedly poked fun at science spam advertising poor quality for-profit "journals", and I have cited an article that claimed it would become difficult for some universities to evaluate scientists' resumes due to the meteoric rise of legit-sounding pretend-journals. I really do not "get" any of this.

That is to say, I do not get why a significant number of people would be willing or foolish enough to submit their manuscripts to pretend-journals, by extension how these pretend-journals can be profitable enough to the spammers for them to continue spamming (many of these "journals" have few to no articles and sometimes the few articles they have are plagiarized from elsewhere so presumably they cannot earn a lot of fees), and finally why anybody would find it hard to know the good journals in their field.

When you start out as a scientist (or scholar) you generally obtain a decent university education and write your thesis under a hopefully competent supervisor. The supervisor will be able to teach you not only how to write a decent paper but also to what journal to submit it. By extension, they will teach you what the good journals in the field are and what kind of "publication strategy" is expected of you if you want to become a career scientist/scholar in the field. In addition to your supervisor, can talk with other colleagues and learn from them. Finally, the papers you needed to read to prepare for your thesis as well as the reference list of said thesis will also give you a clear idea of where the relevant literature in your field is published.

Botany picture #64: Epacris purpurascens

Epacris purpurascens (Ericaceae), Australian National Botanic Garden, 2013. The epacrids are a southern hemisphere clade of the Ericaceae that was once treated as its own family. However, although there are a few freakishly aberrant genera that look more like monocots than like Ericaceae, the differences between epacrids as a whole and the other Ericaceae are actually very small: the loss of one ring of stamens and, in most but not all cases, parallel leaf venation. This particular species has the fairly typical ericaceous habit: a smallish shrub with small, hard leaves and small, radiate flowers.

Reference managers

So far I have lived in the grey zone where the investment that would have been necessary to start using a reference manager appeared just a wee bit larger than the hassle of not using one. But after this Monday I am coming round to it.

The problem that reference managers solve is not so much having to add references to a manuscript per se - one still has to remember which was which to selected the right one, after all - but rather constantly having to format and reformat reference lists at the end of manuscripts. Every journal has its own idea of how a reference should look like. A few examples:

Smith A, Miller B, Ngyuen C, Kim D, 2009. Some paper title. Journal of Research 15: 42-48.

Smith A, Miller B, Ngyuen C, Kim D (2009) Some paper title. Journal of Research 15: 42-48.

Smith A, Miller B, Ngyuen C, Kim D (2009) Some paper title. J. Res. 15:42-48.

Smith, A., Miller, B., Ngyuen, C., Kim, D. (2009). Some paper title. Journal of Research 15: 42-48.

Smith, A., Miller, B., Ngyuen, C., Kim, D. (2009). Some paper title. Journal of Research, 15, 42-48.

Smith, A., B. Miller, C. Ngyuen & D. Kim (2009). Some paper title. Journal of Research 15: 42-48.

Smith A et al., 2009. J. Res. 15: 42-48.

And all possible combinations of the above and more! You can imagine that having to manually format all this for dozens of references gets tedious at some point. A reference manager does all that automatically for you, but of course you first have to import into it all the references you need and you have to provide it with the correct style information for the journal you want to submit a given manuscript to. And because I hopped so much from one study group to the next and from one methodology to the next during my career it never seemed profitable to import references and double check them to use them only in one, two or perhaps three manuscripts.

Because I now expect to work on the same plant family for a long time, and after having gone through a particularly annoying bit of reformatting, I have decided to start using the freeware reference manager Zotero with which I had already dabbled a bit a few years ago. Still, the trouble is the same as what put me off then:

If you don't want to enter all references manually, the easiest way is to import them from a website. Now Zotero is actually really clever at this: if your browser displays search results from Web of Knowledge or Google Scholar, it can open a list of boxes for you to tick and import several references at the same time. Unfortunately, Web of Knowledge finds only a ridiculously small percentage of the references I need and Google Scholar is stupid. I spend a distressing amount of time correcting what is imported from GS because it may provide first names as part of the family name, cities as publishers, paper titles or author names in ALL CAPS, and so on. Still, if I use the same references often enough it will hopefully be worth the effort.

The second problem is styles. Here it would probably pay off if I just invested the money to get EndNote instead, but I want to give Zotero a chance, and the Zotero style repository is simply missing most systematic botany and plant taxonomy journals. I assume I will in time have to figure out how to edit styles for my own purposes.

xkcd: birds and dinosaurs

Just about the most concise explanation of why phylogenetic systematics makes more sense than the alternatives:

From the webcomic xkcd, with thanks to Jerry Coyne for drawing my attention to it with a recent post on his website.

Settling controversies in science, philosophy and economics

Recently I came across a post by blogger Chris Hallquist in which he described his frustration with philosophy. His major points:

one of the biggest things that stands out is how I realized even big-name philosophers often produce arguments so awful that it’s hard to even say anything interesting about why they’re bad. [...]
A big part of the problem is that nobody seems to know how to resolve any of the major disputes in philosophy. This is closely related to the fact that, as philosopher Peter van Inwagen once said, “philosophers do not agree about anything to speak of.” [...]
The total lack of agreement among philosophers on just about anything is problematic for a couple of reasons. For one, many people would like to be able to settle philosophical disputes by looking at what the experts say, an approach that can make perfect sense on issues where the experts genuinely are agreed. But for any given philosophical dispute, while there may be many philosophers who take a certain position, there will pretty much always be many other philosophers who disagree. It’s safe to assume that anyone who tells you otherwise is trying to pull a fast one.
Another problem, which I detailed in retrospective part 1, is that the lack of agreement on what good philosophy is makes it hard to filter the good philosophy and reward the philosophers who produce it.

Another area comes immediately to mind in which similar problems appear to exist is economics, also known as "the dismal science". In contrast, physicists, chemists, climate scientists, astronomers and geologists agree virtually unanimously on virtually anything of importance in their disciplines. It becomes a bit fuzzier in ecology, evolutionary biology and biogeography but the fact of evolution, for example, is in no doubt whatsoever, something that cannot be said, as Hallquist points out, for any of the major issues in philosophy, nor for a question as fundamental as how to deal with a financial crisis in economics.

So what is the difference? Is philosophy simply fuzzy nonsense, or is it dealing with problems that are simply harder to solve? What about other areas where it seems no agreement is being achieved? I must admit I am not writing this post with a great deal of preparation, but it seems to me that there are, as often, various factors to be taken into account.